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<div class="document" id="change-log">
<h1 class="title">Change log</h1>

<div class="section" id="about">
<h1>About</h1>
<p>This file is design for write the change of this program.</p>
</div>
<div class="section" id="id1">
<h1>2011-05-11</h1>
<ul class="simple">
<li>Fixed a problem in parallel_analysis.py. about calculate the RMSD-Z for a bases group.</li>
</ul>
</div>
<div class="section" id="id2">
<h1>2011-04-02</h1>
<ul class="simple">
<li>write a function named echo, which usage for print and flush.</li>
</ul>
</div>
<div class="section" id="id3">
<h1>2011-03-20</h1>
<ul class="simple">
<li>writes some functions for calculate the RMSD of bases group</li>
</ul>
</div>
<div class="section" id="id4">
<h1>2011-03-18</h1>
<ul class="simple">
<li>rewrite some functions in parallel_analysis</li>
</ul>
</div>
<div class="section" id="id5">
<h1>2011-03-16</h1>
<ul class="simple">
<li>Fixed a problem in Index.py.</li>
</ul>
</div>
<div class="section" id="id6">
<h1>2011-03-07</h1>
<ul class="simple">
<li>Change the version to 0.0.7</li>
<li>Add the entropy4gmx.py to scripts.</li>
</ul>
</div>
<div class="section" id="id7">
<h1>2011-02-28</h1>
<ul class="simple">
<li>Add module PQR in MDPackage package. It's used for read in a one or more pqr file and put
them together.</li>
<li>Modified the Modify_Coor script. It read in a pqr file, check it and save it to another
pqr file.</li>
</ul>
</div>
<div class="section" id="id8">
<h1>2011-02-25</h1>
<ul class="simple">
<li>Modified the script Modify_Coor.py, It's runing now.</li>
</ul>
</div>
<div class="section" id="id9">
<h1>2011-02-24</h1>
<ul class="simple">
<li>Add <strong>entropy4gmx.py</strong> to scripts.</li>
</ul>
</div>
<div class="section" id="id10">
<h1>2011-02-23</h1>
<ul class="simple">
<li>Optimiztied the function <strong>Traj_2_coor()</strong> in Traj module and the script <strong>Trjconv.py</strong>.</li>
</ul>
</div>
<div class="section" id="id11">
<h1>2011-02-22</h1>
<ul class="simple">
<li>Modified a bug in Index module.</li>
<li>Add a script named <strong>Trjconv.py</strong>. It's used for convert a trajectory file to a list of
structure file using the function <strong>Traj_2_coor()</strong> in Traj module.</li>
</ul>
</div>
<div class="section" id="id12">
<h1>2011-02-21</h1>
<ul class="simple">
<li>Modified some bugs in Simple_atom module.</li>
<li>Add a function <strong>Traj_2_coor()</strong> in Traj module. It's read in a trajectory file and write
frames to structure files like *.gro or *.pdb</li>
</ul>
</div>
<div class="section" id="id13">
<h1>2011-02-20</h1>
<ul class="simple">
<li>Modified a bugs in <strong>Index</strong> class. Now in a index list, the list[0] is named <em>system</em>.</li>
<li>Modified the Modify_Coor.py. Now loading a molecular, delete groups and saving it is
aviliable.</li>
</ul>
</div>
<div class="section" id="id14">
<h1>2011-02-18</h1>
<ul class="simple">
<li>Modified a bug in Index.py, change <em>reside</em> to <em>residue</em>.</li>
<li>Add some code in Modify_Coor.py for the command mode, run as <strong>Modify_Coor.py -f &lt;filename1&gt;
-o &lt;filename2&gt;</strong>, It's runing now, but some necessary code are instead by <strong>pass</strong>.</li>
</ul>
</div>
<div class="section" id="id15">
<h1>2011-02-17</h1>
<ul class="simple">
<li>Modified the Simple_atom class, add atom_2_PDBformat() and atom_2_GROformat() functions.</li>
</ul>
</div>
<div class="section" id="id16">
<h1>2011-02-16</h1>
<ul class="simple">
<li>Add <strong>Atomlist_2_Index()</strong> in Index module. This function is used to Create a group list
from a atom list which read from a structure file like gro or pdb.</li>
<li>Created a script file named Modify_Coor.py. which is used to load a structure file and
modified it , like delete some groups or save a index file etc. It's not finished now.</li>
<li>Rewrite the output of PDB format for the atom name.</li>
<li>Created functions for PDB format convert to GRO format and GRO format convert to PDB format.</li>
<li>Change the version to 0.0.6</li>
</ul>
</div>
<div class="section" id="id17">
<h1>2011-02-15</h1>
<ul class="simple">
<li>Change the time scale from frame to ns in Parallel_analysis and Twist_in_GDNA.</li>
</ul>
</div>
<div class="section" id="id18">
<h1>2011-02-12</h1>
<ul class="simple">
<li>Modified the Twist_in_GDNA.py, Using the getopt to analysis the input command arguments.</li>
</ul>
</div>
<div class="section" id="id19">
<h1>2011-02-01</h1>
<ul class="simple">
<li>Finished the function <strong>Get_Segment_list()</strong> in GRO.py.</li>
<li>Modified the module parallel_analysis.py, so both gro file and pdb file are allowd for
coordinate input.</li>
<li>Modified the script file Parallel_analysis.py, so both gro file and pdb file are allowd for
coordinate input.</li>
<li>Change the version to 0.0.5.</li>
</ul>
</div>
<div class="section" id="id20">
<h1>2011-01-25</h1>
<ul class="simple">
<li>Add the Simple_atom class, which contain the atom coordinate and atom sequence information.
so gro and pdb file all can be used in twist_in_GDNA. parallel_analysis also will be changed.</li>
<li>parallel_analysis not finished.</li>
</ul>
</div>
<div class="section" id="id21">
<h1>2011-01-24</h1>
<ul class="simple">
<li>Add the test_da.py to test.py. So the test file can used to test every function.</li>
</ul>
</div>
<div class="section" id="id22">
<h1>2011-01-23</h1>
<ul class="simple">
<li>Finish the function Get_Atom_list() in GRO.py module, and test it in test.py.</li>
</ul>
</div>
<div class="section" id="id23">
<h1>2011-01-22</h1>
<ul class="simple">
<li>Create file GRO.py in MDPackage package. But it's not finished.</li>
<li>Modified the Parallel_analysis.py. Make it check if the input is
invalid.</li>
</ul>
</div>
</div>
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